| 1. Round | 18/08/2012 | Rochdale AFC | - | Northampton Town | 0:0 | ||||
| 2. Round | 21/08/2012 | Northampton Town | - | Rotherham United | 2:1 |  |
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| 3. Round | 25/08/2012 | Northampton Town | - | Southend United | 3:3 | |
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| 4. Round | 01/09/2012 | Plymouth Argyle | - | Northampton Town | 3:2 | |
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| 5. Round | 08/09/2012 | Northampton Town | - | AFC Wimbledon | 2:0 | |
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| 6. Round | 15/09/2012 | Fleetwood Town | - | Northampton Town | 1:0 | ||||
| 7. Round | 18/09/2012 | Dagenham & Redbridge | - | Northampton Town | 0:1 | ||||
| 8. Round | 22/09/2012 | Northampton Town | - | Chesterfield FC | 0:0 | ||||
| 9. Round | 29/09/2012 | Burton Albion | - | Northampton Town | 3:3 | |
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| 10. Round | 02/10/2012 | Northampton Town | - | Gillingham FC | 1:2 | ||||
| 11. Round | 06/10/2012 | Bristol Rovers | - | Northampton Town | 3:1 | |
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| 12. Round | 13/10/2012 | Northampton Town | - | Exeter City | 3:0 | |
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| 13. Round | 19/10/2012 | Barnet FC | - | Northampton Town | 4:0 | ||||
| 14. Round | 23/10/2012 | Northampton Town | - | Bradford City | 0:1 | ||||
| 15. Round | 27/10/2012 | Northampton Town | - | Port Vale FC | 2:0 | |
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| 29. Round | 19/01/2013 | Northampton Town | - | Burton Albion | 1:0 | ||||
| 44. Round | 13/04/2013 | Northampton Town | - | York City | 0:2 |
England